S.E.E.S, standing for Specialized Extracurricular Execution Squad, is an extracurricular club at Gekkoukan High School. While the school sponsors them and lists them as a school club, their true purpose is to eliminate the Shadows and investigate both Tartarus and the Dark Hour. Their adviser is Shuji Ikutsuki, while Mitsuru Kirijo functions as the club leader. This group goes into the Dark Hour to learn about its existence and what they can do to prevent the deaths that happen because of it. Each of these members can officially use their Personas, verses Strega, an opposing team, who were artificially able to have these powers.

Junpei's closest relationship in S.E.E.S is with the Protagonist, Minato, or whatever you'd like to name him (For this site I will refer to him as Minato). From the beginning, he tried to relate to Minato because Junpei knew exactly what it felt like to be the "new guy," since he also transferred into the school system late, but as an 8th-grader. When Junpei enters the group, he immediately nominates himself to be the leader, but he is turned down by the others. Akihiko feels like Minato would be the best fit for the leadership role because he's already had experience fighting in the Dark Hour. During one of the first missions, Junpei gets angry listening to Minato make all of the calls, so he decides to run off by himself to fight and be the hero. Junpei's lack of planning makes him ultimately fail, as he ends up needing Minato for protection. He also gets annoyed by how smart Minato is during midterms and class. This causes an emotional break down for Junpei, making it hard for him to believe in himself. He calls himself "worthless" because he can't even be the best at fighting. It isn't until the death of Chidori that Junpei realizes he doesn't need to feel belittled by Minato, and then they finally become better friends.

Junpei becomes very interested in the ghost stories that are being talked about around the school. He tells the group that he wants to be the hero and find the missing girl, Fuuka. He tells them that he knows what she looks like, and that her face looks so "weak" that it makes him want to protect her without even knowing her. When he finds out that there were girls in the school who bullied her, he gets angry. He starts getting defensive about her without even knowing her at all. After the addition of Fuuka to the team, he comments on how cute she looks in her bikini when they are on Summer vacation. After the death of Chidori, Fuuka and Junpei have a cute inspirational conversation. On December 27, Junpei goes into the town to the place where he normally would meet Chidori to think about life. Fuuka approaches him and he tells her that he likes to sit here because it reminds him of Chidori. Junpei stops talking about the past, and tells Fuuka that she's really changed for the better. She gets embarrassed, turning red, as he continues to explain to her that she went from timid to a strong woman. Fuuka encourages him to not underestimate his own growth. Junpei, displeased with her compliment, calls himself a wuss. Fuuka says its not true and goes on to explain, "You're scared because you're not running away... that's nothing to be ashamed of." He responds, "You're really something, Fuuka," as he turns all red. They both agree to keep on fighting and grow stronger for the better good.

Regardless of the differences amongst the team, they are all together because they believe in a similar cause. Yukari and Junpei started off as just school acquaintances who teased each other, and ended up as basically brother and sister. Junpei watched Akihiko from afar and loved how cool he looked, wanting to have the same charm he had with all the ladies. In the end, they became like brothers, able to learn and support each other as equals on the battle field. They even are able to learn from each other on how to get ladies on the beach. Mitsuru was always intimidating for Junpei. He commented on how you have to be extremely smart to hang out with her, and that is why he'd never have a chance. He ended up living under the same roof as her, as they supported each other as well. Mitsuru shows compassion towards Junpei when she thinks that Junpei's room was broken into, or that he was kidnapped. However, it was just a misunderstanding: Junpei is actually just a slob! Ken looked up to Junpei as an older brother. Junpei takes Korumaro on walks daily and always was around him. This was a group of friends and bonds that would always be unbreakable. They learned from each other, they fought beside each other, and they made it.

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